[gmx-users] rtp use

Dallas B. Warren Dallas.Warren at vcp.monash.edu.au
Fri Oct 13 02:04:34 CEST 2006


> I am performing the md on glutathione s-transferase bound to 
> ethacrine.  I was trying to use 'option 0' within pdb2gmx.  I 
> received an error concerning GTT.  This is glutathione which 
> is not represented in the Gff file.

All gobbledegook to me.  I ain't a protein person ;-)
> I extracted the co-ords. from my pdb.  This gave me the 
> glutahione pdb, from which I generated the topology using prodrg.

Take care with what forcefield you are using (i.e. option 0, don't know
what it is now, but used to be ffgmx which is a ff that shouldn't be
used for any research work, there are more developed and superior ones
to that one, see the emailing list for more discussion on that).  Is it
one that is applicable for the system you are simulated?  Is the
parameters you got via prodrg compatable i.e. the same forcefield?
> Now, do I need to make a .rtp entry for this to enable me to 
> use pdb2gmx for the transferase?  If so, what's the easiest 
> way? Thanks.

If there is one residue within your protein and you don't have to use it
again some time down the track on another protein, then you can simply
use the .itp file generated by prodrg and include it (using the include
command) in your topology file.

If there are more than one and any proteins down the track will also use
that same residue, then may be better to generate a rtp file entry to
make things faster/easier for you in the future.

I would recommend you search this emailing list, there are a number of
discussions by those much more in the know than me on this topic.

Hope that is of some assistance.

Catch ya,

Dr. Dallas Warren
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at vcp.monash.edu.au
+61 3 9903 9524
When the only tool you own is a hammer, every problem begins to resemble
a nail.

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